Orsal axes. The right plot shows the number of genes of
Orsal axes. The right plot shows the number of genes of the pathway that belong to a spatial expression cluster. The spatial expression cluster 9 is the only spatial expression cluster in which an overrepresentation was found (KEGG pathway “Ribosome”). (PDF 1595 kb) Additional file 17: Spike in controls were added to the samples and were hybridized to specific probes on the array. Based on the application of 3 widely used normalization methods and the resulting variance we decided to apply quantile normalization in this analysis. (PDF 13 kb) Additional file 18: Example of the determination of a stopping point and a starting point. For an explanation see Methods, paragraph “Identification of starting and stopping points”. lf1 = linear fit on all samples; lof1 = lowest fit on all samples; grey lines indicate intersect of lf1 and lof1; L1: embryo with the largest difference between lf1 and lof1; for stopping genes lf2 = linear fit of L1 to 179; for starting genes lf2 = linear fit of 1 to L1; embryos marked with an asterisk: `not present’ probes in the last (stopping) 15 respectively in the first (starting) 15 embryos; horizontal black line: median probe intensity of embryos marked with an asterisk; dashed line: intersect of lf2 and the horizontal black line indicating the stopping PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28388412 respectively the starting point. (PDF 131 kb)Abbreviations CAM: Cell adhesion molecules; DEC: Dierexperimentencommissie PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 (Animal Welfare Committee); DEG: Differentially Expressed Genes; DFTL: Distance to the Fitted Line; hpf: Hours post fertilization; lf: Linear fit; lof: Lowess fit; MBT: Mid Blastula Transition; MZT: Maternal-to-zygotic Transition; PCA: Principal component analysis; RI plots: Ratio-intensity plotsAcknowledgments We would like to thank Prof. Dr. Annemarie Meijer and Dr. Marcel Schaaf for their hospitality and kind assistance at the Leiden University.Rauwerda et al. BMC Genomics (2017) 18:Page 14 ofFunding The University of Amsterdam has provided the funding for this work, but had no role as such in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Availability of data and materials The datasets generated and/or analysed during the current study are available in the NCBI’s Gene Expression Omnibus with accession number GSE83395: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83395 and through http://rnabiology.nl/Dr-Browser.html. Authors’ RG7666 chemical information contributions Conceived and designed the experiments: HR, MdJ HS TB. Performed the experiments: HR, MdJ, WE, UN. Analyzed the data: HR, JP, WdL, MJ, TB. Contributed reagents/materials/analysis tools: UN, JP, WdL. Wrote the paper: HR, TB. All authors reviewed the manuscript. All authors read and approved the final manuscript. Competing interests The authors declare that they have no competing interests. Consent for publication Not applicable.7.8.9.10.11.12. Ethics approval The local animal welfare committee (DEC) of the University of Leiden, the Netherlands specifically approved this study. All protocols adhered to the international guidelines specified by the EU Animal Protection Directive 86/609/EEC.13.Publisher’s NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Author details 1 RNA Biology Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. 2Institute Biology Leiden, Faculty of Science, Le.